Mercurial > repos > bgruening > openbabel_svg_depiction
view remove_protonation_state.py @ 14:7672039a0bb0 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 327c29cc43f56d7067ab9fa51323ea31951db98b"
author | bgruening |
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date | Tue, 10 Nov 2020 20:40:46 +0000 |
parents | a66827fc370d |
children | 75ee9c410951 |
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#!/usr/bin/env python """ Input: molecular input file. Output: Molecule file with removed ions and fragments. Copyright 2013, Bjoern Gruening and Xavier Lucas """ import argparse from openbabel import openbabel, pybel openbabel.obErrorLog.StopLogging() def parse_command_line(): parser = argparse.ArgumentParser() parser.add_argument('--iformat', default='sdf', help='input file format') parser.add_argument('-i', '--input', required=True, help='input file name') parser.add_argument('-o', '--output', required=True, help='output file name') return parser.parse_args() def remove_protonation(args): outfile = pybel.Outputfile(args.iformat, args.output, overwrite=True) for mol in pybel.readfile(args.iformat, args.input): [atom.OBAtom.SetFormalCharge(0) for atom in mol.atoms] if 'inchi' in mol.data: del mol.data['inchi'] # remove inchi cache so modified mol is saved outfile.write(mol) outfile.close() def __main__(): """ Remove any protonation state from each atom in each molecule. """ args = parse_command_line() remove_protonation(args) if __name__ == "__main__": __main__()